GenotypeAndValidate version 2, ready to be used.
- now it differentiates between confident REF calls and not confident calls. - you can now use a BAM file as the truth set. - output is much clearer now dataProcessingPipeline version 2, ready to be used. - All the processing is now done at the sample level - Reads the input bam file headers to combine all lanes of the same sample. - Cleaning is now scattered/gathered. Inteligently breaks down in as many intervals as possible, given the dataset. - Outputs one processed bam file per sample (and a .list file with all processed files listed) - Much faster, low pass (read Papuans) can run in the hour queue. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5493 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro
parent
687b2e51b4
commit
28149e5c5e
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@ -64,4 +64,26 @@ public class VariantCallContext extends VariantContext {
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public void setRefBase(byte ref) {
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this.refBase = ref;
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}
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/* these methods are only implemented for GENOTYPE_GIVEN_ALLELES MODE */
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//todo -- expand these methods to all modes
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/**
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*
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* @param callConfidenceThreshold the Unified Argument Collection STANDARD_CONFIDENCE_FOR_CALLING
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* @return true if call was confidently ref
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*/
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public boolean isCalledRef(double callConfidenceThreshold) {
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return (confidentlyCalled && (getPhredScaledQual() < callConfidenceThreshold));
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}
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/**
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*
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* @param callConfidenceThreshold the Unified Argument Collection STANDARD_CONFIDENCE_FOR_CALLING
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* @return true if call was confidently alt
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*/
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public boolean isCalledAlt(double callConfidenceThreshold) {
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return (confidentlyCalled && (getPhredScaledQual() > callConfidenceThreshold));
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}
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}
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@ -25,6 +25,8 @@
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package org.broadinstitute.sting.playground.gatk.walkers;
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import org.broad.tribble.util.variantcontext.Allele;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.MutableVariantContext;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.VCFHeader;
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@ -66,11 +68,14 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
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@Reference(window=@Window(start=-200,stop=200))
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public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalker.CountedData, GenotypeAndValidateWalker.CountedData> {
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public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalker.CountedData, GenotypeAndValidateWalker.CountedData> implements TreeReducible<GenotypeAndValidateWalker.CountedData> {
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@Output(doc="File to which validated variants should be written", required=true)
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@Output(doc="File to which validated variants should be written", required=false)
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protected VCFWriter vcfWriter = null;
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@Argument(fullName ="set_bam_truth", shortName ="bt", doc="Use the calls on the reads (bam file) as the truth dataset and validate the calls on the VCF", required=false)
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private boolean bamIsTruth = false;
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@Argument(fullName="minimum_base_quality_score", shortName="mbq", doc="Minimum base quality score for calling a genotype", required=false)
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private int mbq = -1;
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@ -86,32 +91,35 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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@Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false)
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private int minDepth = -1;
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@Argument(fullName ="sample", shortName ="sn", doc="Name of the sample to validate (in case your VCF/BAM has more than one sample)", required=false)
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private String sample = "";
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private String compName = "alleles";
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private UnifiedGenotyperEngine snpEngine;
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private UnifiedGenotyperEngine indelEngine;
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public static class CountedData {
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private long numTP = 0L;
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private long numTN = 0L;
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private long numFP = 0L;
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private long numFN = 0L;
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private long numUncovered = 0L;
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private long numConfidentCalls = 0L;
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private long numNotConfidentCalls = 0L;
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private long nAltCalledAlt = 0L;
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private long nAltCalledRef = 0L;
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private long nRefCalledAlt = 0L;
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private long nRefCalledRef = 0L;
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private long nNotConfidentCalls = 0L;
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private long nUncovered = 0L;
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/**
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* Adds the values of other to this, returning this
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* @param other the other object
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*/
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public void add(CountedData other) {
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numTP += other.numTP;
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numTN += other.numTN;
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numFP += other.numFP;
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numFN += other.numFN;
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numUncovered += other.numUncovered;
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numNotConfidentCalls += other.numNotConfidentCalls;
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numConfidentCalls += other.numConfidentCalls;
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nAltCalledAlt += other.nAltCalledAlt;
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nAltCalledRef += other.nAltCalledRef;
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nRefCalledAlt += other.nRefCalledAlt;
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nRefCalledRef += other.nRefCalledRef;
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nUncovered += other.nUncovered;
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nNotConfidentCalls += other.nNotConfidentCalls;
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}
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}
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@ -133,28 +141,31 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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// Initialize VCF header
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Map<String, VCFHeader> header = VCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), compName);
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Set<String> samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
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Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), logger);
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headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
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vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
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if (vcfWriter != null) {
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Map<String, VCFHeader> header = VCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), compName);
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Set<String> samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
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Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), logger);
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headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
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vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
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}
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// Filling in SNP calling arguments for UG
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UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
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uac.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
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uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
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if (!bamIsTruth) uac.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
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if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
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if (deletions >= 0) uac.MAX_DELETION_FRACTION = deletions;
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if (callConf >= 0) uac.STANDARD_CONFIDENCE_FOR_CALLING = callConf;
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if (emitConf >= 0) uac.STANDARD_CONFIDENCE_FOR_EMITTING = emitConf;
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if (callConf >= 0) uac.STANDARD_CONFIDENCE_FOR_CALLING = callConf;
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snpEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
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// Adding the INDEL calling arguments for UG
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uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.DINDEL;
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indelEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
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// make sure we have callConf set to the threshold set by the UAC so we can use it later.
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callConf = uac.STANDARD_CONFIDENCE_FOR_CALLING;
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}
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//---------------------------------------------------------------------------------------------------------------
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@ -181,47 +192,74 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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// Do not operate on variants that are not covered to the optional minimum depth
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if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
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counter.numUncovered = 1L;
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counter.nUncovered = 1L;
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return counter;
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}
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if (!vcComp.hasAttribute("GV"))
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throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart());
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VariantCallContext call;
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if ( vcComp.isSNP() )
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call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
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else if ( vcComp.isIndel() ) {
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call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
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// if (call.vc == null) // variant context will be null on an extended indel event and I just want to call it one event.
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// return counter;
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}
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else {
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logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
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return counter;
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}
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if (!call.confidentlyCalled) {
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counter.numNotConfidentCalls = 1L;
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if (vcComp.getAttribute("GV").equals("T"))
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counter.numFN = 1L;
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else
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counter.numTN = 1L;
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if (bamIsTruth) {
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if (call.confidentlyCalled) {
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// If truth is a confident REF call
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if (call.isVariant()) {
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if (vcComp.isVariant())
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counter.nAltCalledAlt = 1L; // todo -- may wanna check if the alts called are the same?
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else
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counter.nAltCalledRef = 1L;
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}
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// If truth is a confident ALT call
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else {
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if (vcComp.isVariant())
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counter.nRefCalledAlt = 1L;
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else
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counter.nRefCalledRef = 1L;
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}
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}
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else {
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counter.nNotConfidentCalls = 1L;
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}
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}
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else {
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counter.numConfidentCalls = 1L;
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if (vcComp.getAttribute("GV").equals("T"))
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counter.numTP = 1L;
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if (!vcComp.hasAttribute("GV"))
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throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart());
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if (call.isCalledAlt(callConf)) {
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if (vcComp.getAttribute("GV").equals("T"))
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counter.nAltCalledAlt = 1L;
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else
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counter.nRefCalledAlt = 1L;
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}
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else if (call.isCalledRef(callConf)) {
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if (vcComp.getAttribute("GV").equals("T"))
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counter.nAltCalledRef = 1L;
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else
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counter.nRefCalledRef = 1L;
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}
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else {
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counter.nNotConfidentCalls = 1L;
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}
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}
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if (vcfWriter != null) {
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if (!vcComp.hasAttribute("callStatus")) {
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MutableVariantContext mvc = new MutableVariantContext(vcComp);
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mvc.putAttribute("callStatus", call.isCalledAlt(callConf) ? "ALT" : "REF" );
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vcfWriter.add(mvc, ref.getBase());
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}
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else
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counter.numFP = 1L;
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vcfWriter.add(vcComp, ref.getBase());
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}
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if (!vcComp.hasAttribute("callStatus")) {
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MutableVariantContext mvc = new MutableVariantContext(vcComp);
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mvc.putAttribute("callStatus", call.confidentlyCalled ? "confident" : "notConfident" );
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vcfWriter.add(mvc, ref.getBase());
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}
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else
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vcfWriter.add(vcComp, ref.getBase());
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return counter;
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}
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@ -235,17 +273,22 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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return new CountedData();
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}
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public CountedData treeReduce( final CountedData sum1, final CountedData sum2) {
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sum2.add(sum1);
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return sum2;
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}
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public CountedData reduce( final CountedData mapValue, final CountedData reduceSum ) {
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reduceSum.add(mapValue);
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return reduceSum;
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}
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public void onTraversalDone( CountedData reduceSum ) {
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double ppv = 100 * ((double) reduceSum.numTP /( reduceSum.numTP + reduceSum.numFP));
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double npv = 100 * ((double) reduceSum.numTN /( reduceSum.numTN + reduceSum.numFN));
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double ppv = 100 * ((double) reduceSum.nAltCalledAlt /( reduceSum.nAltCalledAlt + reduceSum.nRefCalledAlt));
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double npv = 100 * ((double) reduceSum.nRefCalledRef /( reduceSum.nRefCalledRef + reduceSum.nAltCalledRef));
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logger.info(String.format("Resulting Truth Table Output\n\n" +
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"---------------------------------------------------\n" +
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"\t\t|\tT\t|\tF\t\n" +
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"\t\t|\tALT\t|\tREF\t\n" +
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"---------------------------------------------------\n" +
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"called alt\t|\t%d\t|\t%d\n" +
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"called ref\t|\t%d\t|\t%d\n" +
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@ -253,20 +296,8 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
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"positive predictive value: %f%%\n" +
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"negative predictive value: %f%%\n" +
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"---------------------------------------------------\n" +
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"uncovered: %d\n" +
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"---------------------------------------------------\n", reduceSum.numTP, reduceSum.numFP, reduceSum.numFN, reduceSum.numTN, ppv, npv, reduceSum.numUncovered));
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/*
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logger.info("called / true = " + reduceSum.numTP);
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logger.info("not called / false = " + reduceSum.numTN);
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logger.info("called /false = " + reduceSum.numFP);
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logger.info("not called / true = " + reduceSum.numFN);
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logger.info("PPV = " + 100 * ((double) reduceSum.numTP /( reduceSum.numTP + reduceSum.numFP)) + "%");
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logger.info("NPV = " + 100 * ((double) reduceSum.numTN /( reduceSum.numTN + reduceSum.numFN)) + "%");
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logger.info("confidently called = " + reduceSum.numConfidentCalls);
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logger.info("not confidently called = " + reduceSum.numNotConfidentCalls );
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logger.info("Uncovered = " + reduceSum.numUncovered);
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*/
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"not confident: %d\n" +
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"not covered: %d\n" +
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"---------------------------------------------------\n", reduceSum.nAltCalledAlt, reduceSum.nRefCalledAlt, reduceSum.nAltCalledRef, reduceSum.nRefCalledRef, ppv, npv, reduceSum.nNotConfidentCalls, reduceSum.nUncovered));
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}
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}
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@ -7,6 +7,7 @@ import org.broadinstitute.sting.queue.function.ListWriterFunction
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import net.sf.samtools.{SAMFileReader,SAMFileHeader,SAMReadGroupRecord}
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import collection.JavaConversions._
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import org.broadinstitute.sting.commandline.ArgumentSource
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class dataProcessingV2 extends QScript {
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@ -27,6 +28,9 @@ class dataProcessingV2 extends QScript {
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@Input(doc="path to R resources folder inside the Sting repository", shortName="r", required=true)
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var R: String = _
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@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", shortName="bwa", required=false)
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var bwaPath: File = _
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@Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
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var input: File = _
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@ -57,24 +61,42 @@ class dataProcessingV2 extends QScript {
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@Input(doc="output bams at intervals only", shortName="intervals", required=false)
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var intervals: File = _
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// Gracefully hide Queue's output
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val queueLogDir: String = ".qlog/"
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// Use the number of contigs for scatter gathering jobs
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var nContigs: Int = -1
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def script = {
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// Helpful variables
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// Updates and checks that all input files have the same number of contigs
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// we use the number of contigs for scatter gather.
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def updateNumberOfContigs(n: Int): Boolean = {
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if (nContigs < 0) {
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nContigs = n
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return true
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}
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return nContigs == n
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}
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def createSampleFiles(): Map[String, File] = {
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val outName: String = qscript.outputDir + qscript.projectName
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//todo -- process bam headers to compile bamLists of samples.
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var sampleTable = scala.collection.mutable.Map.empty[String, List[File]]
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// Creating a table with SAMPLE information from each input BAM file
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val sampleTable = scala.collection.mutable.Map.empty[String, List[File]]
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for (bam <- scala.io.Source.fromFile(input).getLines) {
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val bamFile = new File(bam)
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val samReader = new SAMFileReader(bamFile)
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val header = samReader.getFileHeader()
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val readGroup = header.getReadGroups()
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for (rg <- readGroup) {
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// keep a record of the number of contigs in this bam file (they should all be the same
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assert(updateNumberOfContigs(header.getSequenceDictionary.getSequences.size()), "Input BAMS should all have the same number of contigs. " + bam + " has " + header.getSequenceDictionary.getSequences.size())
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val readGroups = header.getReadGroups()
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// only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
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// with PrintReads to separate the samples. Tell user to do it himself!
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assert(hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
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// Fill out the sample table with the readgroups in this file
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for (rg <- readGroups) {
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val sample = rg.getSample()
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if (!sampleTable.contains(sample))
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sampleTable(sample) = List(bamFile)
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@ -83,22 +105,36 @@ class dataProcessingV2 extends QScript {
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}
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}
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// Creating one file for each sample in the dataset
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val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
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for ((sample, flist) <- sampleTable) {
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val sampleFileName = new File(outName + "." + sample + ".bam")
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sampleBamFiles(sample) = sampleFileName
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add(joinBams(flist, sampleFileName))
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}
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return sampleBamFiles.toMap
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}
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println("\nFound the following samples (files created as necessary): ")
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def script = {
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//todo -- (option - BWA) run BWA on each bam file (per lane bam file) before performing per sample processing
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var cohortList: List[File] = List()
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val sampleBamFiles = createSampleFiles()
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// Simple progress report
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println("\nFound the following samples: ")
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for ((sample, file) <- sampleBamFiles)
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println("\t" + sample + " -> " + file)
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val globalIntervals = new File(outName + ".intervals")
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// If this is a 'knowns only' indel realignment run, do it only once for all samples.
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val globalIntervals = new File(outputDir + projectName + ".intervals")
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if (knownsOnly)
|
||||
add(target(null, globalIntervals))
|
||||
|
||||
// Put each sample through the pipeline
|
||||
for ((sample, bam) <- sampleBamFiles) {
|
||||
|
||||
// BAM files generated by the pipeline
|
||||
|
|
@ -124,7 +160,13 @@ class dataProcessingV2 extends QScript {
|
|||
cov(recalBam, postRecalFile),
|
||||
analyzeCovariates(preRecalFile, preOutPath),
|
||||
analyzeCovariates(postRecalFile, postOutPath))
|
||||
|
||||
cohortList :+= recalBam
|
||||
}
|
||||
|
||||
// output a BAM list with all the processed per sample files
|
||||
val cohortFile = new File(qscript.outputDir + qscript.projectName + ".cohort.list")
|
||||
add(writeList(cohortList, cohortFile))
|
||||
}
|
||||
|
||||
// General arguments to all programs
|
||||
|
|
@ -142,9 +184,9 @@ class dataProcessingV2 extends QScript {
|
|||
override def inputBams = join
|
||||
override def outputBam = joined
|
||||
override def commandLine = super.commandLine + " CREATE_INDEX=true"
|
||||
this.memoryLimit = Some(6)
|
||||
this.jarFile = qscript.mergeBamJar
|
||||
this.isIntermediate = true
|
||||
this.analysisName = queueLogDir + outBam + ".joinBams"
|
||||
this.jobName = queueLogDir + outBam + ".joinBams"
|
||||
}
|
||||
|
||||
|
|
@ -155,6 +197,8 @@ class dataProcessingV2 extends QScript {
|
|||
this.mismatchFraction = Some(0.0)
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
|
||||
this.rodBind :+= RodBind("indels", "VCF", indels)
|
||||
this.scatterCount = nContigs
|
||||
this.analysisName = queueLogDir + outIntervals + ".target"
|
||||
this.jobName = queueLogDir + outIntervals + ".target"
|
||||
}
|
||||
|
||||
|
|
@ -168,6 +212,8 @@ class dataProcessingV2 extends QScript {
|
|||
this.doNotUseSW = useSW
|
||||
this.compress = Some(0)
|
||||
this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
|
||||
this.scatterCount = nContigs
|
||||
this.analysisName = queueLogDir + outBam + ".clean"
|
||||
this.jobName = queueLogDir + outBam + ".clean"
|
||||
}
|
||||
|
||||
|
|
@ -182,15 +228,17 @@ class dataProcessingV2 extends QScript {
|
|||
sortOrder = null
|
||||
this.memoryLimit = Some(6)
|
||||
this.jarFile = qscript.dedupJar
|
||||
this.isIntermediate = true
|
||||
this.analysisName = queueLogDir + outBam + ".dedup"
|
||||
this.jobName = queueLogDir + outBam + ".dedup"
|
||||
}
|
||||
|
||||
//todo -- add scatter gather capability (waiting for khalid's modifications to the queue base
|
||||
case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
|
||||
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
|
||||
this.input_file :+= inBam
|
||||
this.recal_file = outRecalFile
|
||||
this.analysisName = queueLogDir + outRecalFile + ".covariates"
|
||||
this.jobName = queueLogDir + outRecalFile + ".covariates"
|
||||
}
|
||||
|
||||
|
|
@ -204,7 +252,9 @@ class dataProcessingV2 extends QScript {
|
|||
else if (qscript.intervals != null) this.intervals :+= qscript.intervals
|
||||
this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
|
||||
this.index_output_bam_on_the_fly = Some(true)
|
||||
this.analysisName = queueLogDir + outBam + ".recalibration"
|
||||
this.jobName = queueLogDir + outBam + ".recalibration"
|
||||
|
||||
}
|
||||
|
||||
case class analyzeCovariates (inRecalFile: File, outPath: File) extends AnalyzeCovariates {
|
||||
|
|
@ -212,12 +262,16 @@ class dataProcessingV2 extends QScript {
|
|||
this.resources = qscript.R
|
||||
this.recal_file = inRecalFile
|
||||
this.output_dir = outPath.toString
|
||||
this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
|
||||
this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
|
||||
}
|
||||
|
||||
case class writeList(inBams: List[File], outBamList: File) extends ListWriterFunction {
|
||||
this.inputFiles = inBams
|
||||
this.listFile = outBamList
|
||||
this.analysisName = queueLogDir + outBamList + ".bamList"
|
||||
this.jobName = queueLogDir + outBamList + ".bamList"
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue